The best way to follow this discussion is to sit in front of a Linux Terminal and try the examples while you read. Turn on your machine, fire up a shell and put your hands on the keyboard, NOW ;-).

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If you have read the previous section of this book, you are now familiar with at least three Linux shell commands, "​pwd",​ "​cd"​ and "​ls"​. You have learned that commands can, sometimes optionally, take an **argument** (ls /etc) and also some **options** (ls -la /etc). The options are usually preceded by a minus "​-"​ symbol (-la).

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So while some commands are extremely simple and linear to use, the addition of options and arguments can turn them into powerful and flexible tools.

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An in-depth, nice and clean guide of the main linux commands is available online thanks to the [[http://​www.linfo.org/​command_index.html|Linux Information Project Linux Commands pages]].

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We will now list the main Linux commands in what we consider a logical order, rather than alphabetically.

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==== man ====

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Linux commands are generally documented in detail. If you want to know everything about the arguments and the options of a particular command you can use the "​man"​ command, that takes as an argument the name of the command on which you wish to have information. Let's use it to get information on the "​ls"​ list command:

On man pages, you can press the space bar to read more, if all the contents do not fit into your current view of the Terminal window. Press "​q"​ to exit the man page and go back to the prompt.

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==== touch ====

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''​andrea@ubuntu:​~$ touch my_sequence.fasta''​

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You can use the "​touch"​ command to create one or more files on the fly. In the example above you create a file called "​my_sequence.fasta"​ in the current directory. If the current directory contains a subdirectory called "​sequences"​ you could create the file inside this subdirectory,​ by providing the relative path of the file to be created as "​touch"​ argument:

You can also use touch to manipulate timestamps of existing files or new files, but this is beyond the scope of this course. Learn more:

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* [[http://​www.linfo.org/​touch.html|"​touch"​ on Linux Info]]

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==== mkdir ====

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if the "​sequences"​ directory does not exist, you can create it with the "​mkdir"​ __M__a__k__e __Dir__ectory shell command.

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''​andrea@ubuntu:​~$ mkdir sequences''​

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You can create several directories at once:

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''​andrea@ubuntu:​~$ mkdir sequences1 sequences2 ...''​

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With the "​m"​ option you can assign a specific permission at creation time

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''​andrea@ubuntu:​~$ mkdir -m 777 sequences''​

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You can create a directory inside other directories that still do not exist, thereby creating a full directory hierarchy with a single command, with the "​p"​ option:

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''​andrea@ubuntu:​~$ mkdir -p bioinfo/​sequences/​processed/​dna''​

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==== rm and rmdir====

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The "​rm"​ __r__e__m__ove shell command can be use to delete files. It can also delete directories (with the -r option) and be used as an alternative to the more specific "​rmdir"​ __r__e__m__ove __dir__ectory command for deleting directories. "​rm"​ deletes the files without asking for a confirmation.

In order to delete a directory, even if not empty, you can use "​rm"​ with the "​rf"​ options:

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''​andrea@ubuntu:​~$ mkdir sequences''​

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''​andrea@ubuntu:​~$ touch sequences/​a-file.txt''​

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''​andrea@ubuntu:​~$ rmdir sequences'' ​ # Using the "​rmdir"​ command on a directory which is not empty will return an error. We can use "rm -rf" instead, which will silently remove the directory and all it's contents, with no complains. See figure 2-3-2 for an example.

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''​andrea@ubuntu:​~$ rm -rf sequences''​

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Exhaustive information on the use of the "​rm"​ and "​rmdir"​ commands can be found here:

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* [[http://​www.linfo.org/​rm.html|"​rm"​ on Linux Info]]

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* [[http://​www.linfo.org/​rmdir.html|"​rmdir"​ on Linux Info]]

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==== cp ====

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The Linux "​cp"​ shell command __c__o__p__y can make a copy of a file.

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It accepts 2 arguments. The first is the path of file to be copied. The second can be either a file name or the name of an existing directory. Depending on the second argument, the result is different. Let's see a couple of examples.

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''​andrea@ubuntu:​~$ copy file1.txt file2.txt''​ # the second argument is a file name

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will make a copy of "​file1.txt"​ and save it with the name "​file2.txt"​.

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''​andrea@ubuntu:​~$ copy file1.txt ..''​ # the second argument is a directory name

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will make a copy of "​file1.txt",​ with the same exact name, to the parent (..) of the present working directory

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==== mv ====

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The "​mv"​ __m__o__v__e shell command can either rename a file (by file we always mean any kind of file, including directories) or move a file to a different directory, depending on whether the second argument is a file name or an existing directory. The first argument is the path of the file to be renamed or moved. Let us go through a couple of examples (see also figure 2-3-2).

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''​andrea@ubuntu:​~$ mv file1.txt file2.txt''​ # the second argument is a file name

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this will rename file1.txt to file2.txt

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''​andrea@ubuntu:​~$ mv file1.txt sequences/​dna''​ # the second argument is a directory

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this will move "​file1.txt"​ from the current directory to the sequences/​dna directory

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''​andrea@ubuntu:​~$ mv * ..''​ # the second argument is a directory

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moves all files of the present working directory up one level, to the parent directory. Indeed, the wildcard character * will match all filenames.

The "​sudo"​ shell command is required to temporarily acquire root privileges on a Linux machine. The root user have the power of performing any action, the normal permission restrictions do not apply to the root user.

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For example, the modification of any Linux system file, including configuration files in the /etc folder require root privileges. Root privileges are also require to stop, start, restart system processes and services.

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For example, restarting the apache web server requires root access, which can be acquired by prefixing the "​sudo"​ command to the command to be issued as root.

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''​andrea@ubuntu:​~$ service apache2 restart''​

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will give an error (you need Apache installed before you try this). Also trying for example to create a file in the root folder will give an error, as normal users do not have the permissions for this. Try:

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''​andrea@ubuntu:​~$ touch /​test.txt''​

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You instead need to use sudo for these operations. Mind that not all users on a machine are "​sudoers"​. Only the system administrator have these privileges, or other users that were selected and enabled as sudoers by the system administrator. We'll see how to grant a user sudo privileges in a moment. By default, when you install Ubuntu you will create a default user, which indeed has administrator privileges.

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When you issue a sudo command for the first time during a session, you will be asked to type your password again, for added security. Subsequent sudo commands will not require a password for a few minutes, after which your magical powers vanish and you have to enter the password again.

You can add users to your machine with the "​adduser"​ shell command. This requires the powers of the system administrator and therefore, sudo:

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''​andrea@ubuntu:​~$ sudo adduser carl''​

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In the process you will be required to type a password for the user ("​Enter new UNIX password:"​) and then to confirm it ("​Retype new UNIX password:"​). You will also be prompted to enter some standard user information (full name, room number ...), that you can also leave blank (see session in figure 2-3-4).

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When the user is created, an home folder for the user will also be created in /​home/​newusername.

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If you want to grant carl administration privileges (that is if you want to add carl to the sudoers list) you can then type, after the user was already created (otherwise you will get an error message complaining that the user does not exist):

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''​andrea@ubuntu:​~$ sudo adduser carl admin''​

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This will add carl to the administrators group.

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You can delete a user with the "​userdel"​ shell command. This will not delete the user home folder though. You can then delete the user home folder, if you wish, with a "rm -rf" command.

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''​andrea@ubuntu:​~$ sudo userdel carl''​

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''​andrea@ubuntu:​~$ sudo rm -rf /​home/​carl''​

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== Figure 2-3-4: Creating and deleting a user with adduser and userdel ==

If you are setting up a server for the course, this could be a good moment to create an account for each student. In another sub-chapter we will see how to configure apache and the userdir apache module so that each user on you machine can have it's own web space to be used for study and applications/​web development purposes.

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==== chmod ====

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The "​chmod"​ shell command allows to change the permissions for a file.

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''​andrea@ubuntu:​~$ chmod 666 textfile.txt''​

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chmod can be used with a different syntax also. For example, to add write permission for all (owner, group, others) you can type:

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''​andrea@ubuntu:​~$ chmod +w textfile.txt''​

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to add write and execute permission for all:

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''​andrea@ubuntu:​~$ chmod +wx textfile.txt''​

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Granting execution privileges to all files ending in .cgi, contained in the present working directory:​

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''​andrea@ubuntu:​~$ chmod +x *.cgi''​

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Granting write privileges, in the present working directory, to all files and directories,​ and the directory contents, by using the recursive option "​R":​

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''​andrea@ubuntu:​~$ chmod -R +w *''​

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You can type:

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''​andrea@ubuntu:​~$ man chmod''​

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to access the chmod man page and all the information on the available options for the command.

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==== chown ====

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With the "​chown"​ shell command you can change the owner of a file:

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''​andrea@ubuntu:​~$ sudo chown carl textfile.txt''​

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You can also use chown to change the group information,​ but this is beyond the scope of this course.

For security and system stability reasons, it is a wise idea, once you have installed Linux on a machine, to keep the OS up to date. On Debian derived systems, such as Ubuntu, this can be done by using the "​apt-get"​ shell command. A typical usage for applying available software updates is as follows:

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''​andrea@ubuntu:​~$ sudo apt-get update''​

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Updates the list of the software repositories,​ from which updates are downloaded. And then:

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''​andrea@ubuntu:​~$ sudo apt-get upgrade''​

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Updates the system to the last software releases, including security updates that are essential to keep your system safe. Don't do it and it will only be a matter of time before your system is compromised/​hacked.

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You can also upgrade to the latest Linux distribution. For example if you have Ubuntu 11.10 (Oneiric Ocelot) installed and want to upgrade to Ubuntu 12.04 (Precise Pangolin), you can use the dist-upgrade option:

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''​andrea@ubuntu:​~$ sudo apt-get dist-upgrade''​

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apt-get can be used to install new software with the "​install"​ option:

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''​andrea@ubuntu:​~$ sudo apt-get install openssh-server''​

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will install the open SSH Server software in your machine. This is something we will need to do to turn our machine in a web server, the procedure will be described in the next sub-chapter.

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You can also remove installed software with the "​remove"​ option:

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''​andrea@ubuntu:​~$ sudo apt-get remove openssh-server''​

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==== nano: the nano text editor ====

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It is quite an essential task for a system administrator to be able to create and edit files right from remote shell connection (more on remote shell connections in the next sub-chapter). If working locally, on a graphical environment,​ there is a wide choice for good code editors. Remotely, while working on a shell, there are two editors that are mostly used: the [[http://​www.nano-editor.org/​|nano text editor]] and the [[http://​heather.cs.ucdavis.edu/​~matloff/​UnixAndC/​Editors/​ViIntro.html|vi text editor]].

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During this course we will use nano, that has a somewhat easier learning curve than vi.

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Typical usage of nano is with the "​w"​ option (no wrap). Failing to use this option can seriously damage your code pages, any code edit should always be edited with the "​w"​ option. The argument is a filepath. if the file already exists it will be opened for editing, otherwise the file will be created.

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Let's open a new file called myseq.fasta:​

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''​andrea@ubuntu:​~$ nano -w myseq.fasta''​

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Nano will open. We can then type some text and save by hitting Ctrl + o, and then hitting return to confirm the filename for the file. We can then exit from nano and get back to the shell prompt by hitting Ctrl + x. The most frequent keyboard shortcuts are listed in the bottom part of the nano window itself, for quick reference In figure 2-3-5 you can see how the nano interface looks like. Concerning the shortcuts at the bottom of the screen, be aware that when you see ^C, it really means: Ctrl + c.

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Useful shortcuts within nano are:

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Ctrl + k

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cuts out a line. You can then move the cursor and paste back the line with

Now that we can create and edit files, let's write a simple "Hello World!"​ script in python and run it.

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Let's first check if python is installed, and where:

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''​andrea@ubuntu:​~$ which python''​

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Python is installed by default on Ubuntu. You should get back something like:

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''/​usr/​bin/​python''​

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Let's create the script file and open it for editing with nano, all in one command:

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''​andrea@ubuntu:​~$ nano -w helloworld.py''​

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We will then put a first line in the script, called [[http://​en.wikipedia.org/​wiki/​Shebang_(Unix)|shebang line]], to point Linux to the correct interpreter for the code that follows. Since we will write in python, we must include the python path returned previously by the "which python"​ command:

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''#​!/​usr/​bin/​python''​

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We can then enter the python code on the second line:

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print "​Hello,​ World!"​

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//The helloworld.py python script//

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<​code>​

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#​!/​usr/​bin/​python

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print "​Hello,​ World!"​

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</​code>​

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That's it, we are done. We can save with Ctrl + o, press return to confirm the file name and then exit nano with Ctrl + x.

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If we try to then run the script like this:

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''​andrea@ubuntu:​~$ ./​helloworld.py''​

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This will not work, because the file does not have execute permissions. Let's grant execute permission:​

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''​andrea@ubuntu:​~$ chmod +x helloworld.py''​

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Then we can execute it:

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''​andrea@ubuntu:​~$ ./​helloworld.py''​

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will print "​Hello,​ World!"​ to the screen. Please note that in order for Linux to understand that we want to run the script file, rather than executing a command with the same name as the script, we have to use the ./ notation for the relative path, or use an absolute path. So we have to type:

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''​andrea@ubuntu:​~$ ./​helloworld.py''​

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or

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''​andrea@ubuntu:​~$ /​home/​andrea/​helloworld.py''​

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rather then:

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''​andrea@ubuntu:​~$ helloworld.py''​

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that will raise an error about the command not existing.

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Congratulations,​ you have just started your journey as an expert programmer, stick with us to build up your web development for bioinformatics programming skills!

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It's now time to move ahead and turn our newly installed Linux distro in a full fledged web server. We will start by installing an SSH Server and learning to connect remotely to our machine. [[chapter_2_-_the_linux_operating_system:​installing and using openssh server for remote connections |Read on]]

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